We have identified 15 highly polymorphic (between 5 and 21 alleles) microsatellite (simple sequence repeat = SSR) loci and estimated frequencies of their alleles in approximately 150 rhesus macaques (Macaca mulatta) from six different breeding colonies in the U.S. For this purpose a new non-radioactive method was developed for resolving PCR amplification products on a short polyacrylamide gel and identifying alleles by estimating fragment size (numbers of base pairs). Parallel analyses of nine electrophoretically defined polymorphic protein coding loci revealed that the level of gene diversity based on the SSR loci was more than twice that based on protein coding loci alone. The new polymorphisms will improve the success of our efforts to study population processes that influence colony productivity because the success of paternity (and maternity) exclusion, required to reconstruct patrilineal (and confirm matrilineal) relationships and estimate kinship and inbreeding coefficients is highly correlated with the level of gene diversity of genetic polymorphisms used for these purposes. One such process is the loss of fitness due to inbreeding depression in populations with insufficient gene flow. Our recent study of fertility, mortality and rate of weight gain in inbred and non-inbred rhesus macaques revealed no evidence of inbreeding depression (loss of fitness) at levels of consanguineous inbreeding approximately equal to half-sib mating (F=0.125), a level at which significant loss of fitness occurs in some captive bred species, including some other species of genus Macaca. In another study we demonstrated that rhesus avoid mating with matrilineal relatives as close as half-sibs but breed randomly with regard to patrilineal relationships and more remote matrilineal relationships. *KEY*Microsatellite (SSR) loci, LCR amplification, Inbreeding, Fitness, Paternity exclusion, Gene diversity